#install.packages("NbClust")
#install.packages("mclust")
#install.packages("factoextra")
#install.packages("DiagrammeR")
#install.packages("rfUtilities")Supervised Machine Learning
1 Installing packages
2 Regression Trees: Boston Housing Data
2.1 Demo with Boston Data
data("Boston")
set.seed(123)
# default RF model: ntree = 500, mtry = nos. of features/3
m1 <- randomForest(formula = log(medv) ~ ., data = Boston, importance=TRUE)
plot(m1)
which.min(m1$mse)[1] 500# Tuning mtry
ForestTune <- caret::train(y=log(Boston[,14]),
x=Boston[,1:13],
tuneGrid=data.frame(mtry=1:10),
method="rf",
ntree=500,
trControl=trainControl(method="oob"))
ForestTuneRandom Forest
506 samples
13 predictor
No pre-processing
Resampling results across tuning parameters:
mtry RMSE Rsquared
1 0.1970465 0.7671552
2 0.1592069 0.8479968
3 0.1492000 0.8665045
4 0.1448385 0.8741952
5 0.1435082 0.8764956
6 0.1442932 0.8751408
7 0.1456864 0.8727179
8 0.1450441 0.8738378
9 0.1482671 0.8681688
10 0.1481130 0.8684425
RMSE was used to select the optimal model using the smallest value.
The final value used for the model was mtry = 5.plot(ForestTune)
m1 <- randomForest(formula = log(medv) ~ ., data = Boston,
ntree=500, mtry = 5, importance=TRUE)
importance(m1) %IncMSE IncNodePurity
crim 22.045081 10.2428053
zn 5.261208 0.2064273
indus 10.185472 2.2999356
chas 3.123448 0.2268523
nox 26.029882 8.4265352
rm 41.678157 16.5194111
age 17.562822 1.9765128
dis 21.341995 4.5182532
rad 7.947701 0.6057602
tax 13.035036 2.5129642
ptratio 14.317925 4.3062644
black 15.466762 1.6596508
lstat 38.190017 29.1222391varImpPlot(m1)
plot(m1)
which.min(m1$mse)[1] 492# Partial dependance plots
par(mfrow=c(1,1))
# Partial plots of single variable
m1 %>%
partial(pred.var = "rm") %>%
plotPartial(smooth = FALSE, lwd=3,
ylab = "Median log Price",
main = "Partial Dependance Plot",
xlab ="Number of Rooms")
partial(m1, pred.var = "rm", plot = TRUE, rug = TRUE) #rug: 
partialPlot(m1, pred.data = Boston, x.var = "rm", rug = TRUE)
# Partial plots of two variables
pd <- partial(m1, pred.var = c("lstat", "rm"))
plotPartial(pd)
# Add contour lines and use a different color palette
rwb <- colorRampPalette(c("red", "white", "blue"))
plotPartial(pd, contour = TRUE, col.regions = rwb,
main ="PDP: % lower status pop vs nos. room", xlab="number of rooms",
ylab ="% lower status of Pop" )
3 Gradient Boosting - Boston Housing Data
set.seed(123)
# train GBM model
gbm1 <- gbm(
formula = log(medv) ~ .,
distribution = "gaussian",
data = Boston,
n.trees = 2000,
interaction.depth = 1,
shrinkage = 0.001,
cv.folds = 5,
n.cores = NULL, # will use all cores by default
verbose = FALSE
)
# Using caret with the default grid to optimize tune parameters automatically
# GBM Tuning parameters:
# n.trees (# Boosting Iterations)
# interaction.depth (Max Tree Depth)
# shrinkage (Shrinkage)
# n.minobsinnode (Min. Terminal Node Size)
# Tuning hyper hyper parameters
hyper_grid <- expand.grid(
n.trees = c(1000, 2000),
shrinkage = c(0.001, .01, .05),
interaction.depth = c(1, 2, 3),
n.minobsinnode = c(10, 20))
trainControl <- trainControl(method="cv", number=10)
set.seed(99)
gbm.caret <- train(log(medv) ~ .
, data=Boston
, distribution="gaussian"
, method="gbm"
, trControl=trainControl
, verbose=FALSE
, tuneGrid=hyper_grid
)
# attributes(gbm.caret)
gbm.caret$bestTune n.trees interaction.depth shrinkage n.minobsinnode
30 2000 2 0.05 10# GBM with tunes hyper parameters
gbm2 <- gbm(
formula = log(medv) ~ .,
distribution = "gaussian",
data = Boston,
n.trees = 2000,
interaction.depth = 2,
shrinkage = 0.05,
n.minobsinnode = 10,
cv.folds = 5,
n.cores = NULL, # will use all cores by default
verbose = FALSE
)
# Variable importance
vip::vip(gbm2)
# PDPs
gbm2 %>%
partial(pred.var = "rm", n.trees = gbm2$n.trees, grid.resolution = 100) %>%
autoplot(rug = TRUE, train = Boston)
gbm2 %>%
partial(pred.var = c("rm", "lstat"), n.trees = gbm2$n.trees, grid.resolution = 100) %>%
autoplot(rug = TRUE, train = Boston)
pd <- partial(gbm2, pred.var = c("rm","lstat"), n.trees = gbm2$n.trees, grid.resolution = 100)
# Add contour lines and use a different color palette
rwb <- colorRampPalette(c("red", "white", "blue"))
plotPartial(pd, contour = TRUE, col.regions = rwb,
main ="PDP: % lower status pop vs nos. room", xlab="% lower status of Pop", ylab ="number of rooms")
4 Classification Trees for Buy-No Buy Data: Eight product categories
data1 = read.csv(here("data", "iridata.csv"))
# Baby,Coffee,Detergent,Paste,Sauce,Snacks,Sunscreen,Tuna
data2 = subset(data1, subset=catno =="Baby")
str(data2)'data.frame': 1225 obs. of 12 variables:
$ catno : chr "Baby" "Baby" "Baby" "Baby" ...
$ hhinc : chr "$100 plus" "$25-49K" "$100 plus" "< 25K" ...
$ hhsize : chr "1-2 members" "3 members" "1-2 members" "1-2 members" ...
$ race : chr "Other" "Caucasian" "Caucasian" "Caucasian" ...
$ ethnicity : chr "Non-Hispanic" "Non-Hispanic" "Non-Hispanic" "Non-Hispanic" ...
$ affluence : chr "Getting By" "Living Comfortably" "Getting By" "Doing Well" ...
$ pres_child : chr "No" "No" "No" "No" ...
$ age_head : chr "55-64Y" "50-54Y" "65+Y" "65+Y" ...
$ educ_fem_head: chr "Some College" "Some or High School" "Post College Grade" "Some or High School" ...
$ census : chr "West" "South" "West" "Central" ...
$ buy : int 0 0 0 0 0 0 0 0 0 0 ...
$ purchase : chr "NO" "NO" "NO" "NO" ...cat_vars <- c("hhinc", "hhsize", "race", "ethnicity", "affluence", "pres_child",
"age_head", "educ_fem_head", "census", "purchase")
data <- data2 %>%
mutate(across(all_of(cat_vars), as_factor))
str(data)'data.frame': 1225 obs. of 12 variables:
$ catno : chr "Baby" "Baby" "Baby" "Baby" ...
$ hhinc : Factor w/ 5 levels "$100 plus","$25-49K",..: 1 2 1 3 3 4 2 1 4 2 ...
$ hhsize : Factor w/ 3 levels "1-2 members",..: 1 2 1 1 1 3 1 3 1 3 ...
$ race : Factor w/ 2 levels "Other","Caucasian": 1 2 2 2 2 2 1 2 2 2 ...
$ ethnicity : Factor w/ 2 levels "Non-Hispanic",..: 1 1 1 1 1 1 1 1 1 1 ...
$ affluence : Factor w/ 3 levels "Getting By","Living Comfortably",..: 1 2 1 3 3 1 1 1 1 3 ...
$ pres_child : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 2 1 2 1 2 ...
$ age_head : Factor w/ 6 levels "55-64Y","50-54Y",..: 1 2 3 3 2 4 1 1 1 5 ...
$ educ_fem_head: Factor w/ 4 levels "Some College",..: 1 2 3 2 2 2 1 3 2 2 ...
$ census : Factor w/ 4 levels "West","South",..: 1 2 1 3 1 1 2 3 2 3 ...
$ buy : int 0 0 0 0 0 0 0 0 0 0 ...
$ purchase : Factor w/ 2 levels "NO","YES": 1 1 1 1 1 1 1 1 1 1 ...# Single Tree: Tuning complexity parameter, cp
TreeTune<-train(y=data[,12],
x=data[,2:10],
tuneGrid=data.frame(cp=seq(.001,.05,length.out = 20)),
method="rpart",
trControl=trainControl(method="repeatedcv",repeats=10,number=10))
TreeTune$bestTune cp
7 0.01647368plot(TreeTune)
# Tree
GoodTree <- rpart(purchase ~ hhinc + hhsize + race + ethnicity +
affluence + pres_child + age_head + educ_fem_head +
census,data=data,method="class",
control=rpart.control(cp=0.01389474))
# summary(GoodTree)
fancyRpartPlot(GoodTree)
onetree <- predict(GoodTree, type="prob")[,2]
rpart.plot(GoodTree, type =5, extra=104, fallen.leaves=T, main="Sample Single Tree")
5 Random Forest NOBuy- Buy Data
# Tuning mtry
ForestTune <- caret::train(y=data[,12],
x=data[,2:10],
tuneGrid=data.frame(mtry=1:6),
method="rf",ntree=500,
trControl=trainControl(method="oob"))
ForestTune$results Accuracy Kappa mtry
1 0.6653061 0.1179931 1
2 0.6693878 0.2433716 2
3 0.6465306 0.1980087 3
4 0.6391837 0.1904641 4
5 0.6359184 0.1865918 5
6 0.6293878 0.1789447 6plot(ForestTune)
m2 <- randomForest(x=data[,2:10],y=data[,12],data=data,
type="classification",ntree=500,mtry=2, importance = TRUE)
# Random Forest prediction
rfpred <- predict(m2,type="prob")[,2]
importance(m2) NO YES MeanDecreaseAccuracy MeanDecreaseGini
hhinc 9.9518220 -0.3497756 7.2112029 35.142585
hhsize 10.9960555 10.5337820 18.7930710 29.110216
race 1.4224556 0.8806341 1.5690573 12.071906
ethnicity 0.1589872 -3.6983692 -3.0587445 8.718574
affluence 3.7526294 -0.8801165 2.3765147 17.028193
pres_child 10.4635617 13.8523152 24.9207270 25.745736
age_head 25.9393002 11.2475624 29.6558953 70.898330
educ_fem_head -5.1915254 4.2517352 -0.1875437 31.587706
census -1.9234697 1.0663672 -0.3993511 32.299178varImpPlot(m2)
# PDP for single variable
partialPlot(x=m2, pred.data=data, x.var=hhsize, which.class="YES")
partialPlot(x=m2, pred.data=data, x.var=pres_child, which.class="YES")
# Household Size
m2 %>%
partial(pred.var="hhsize", prob=TRUE, which.class ="YES" ) %>%
plotPartial(smooth=FALSE, lwd=2, ylab=expression(probability),ylim=c(0.5,0.9), main=expression(Partial.Dependance.Plot(Random.Forest)), xlab=expression(Household.Size))
# Age of Head
m2 %>%
partial(pred.var="pres_child", prob=TRUE, which.class ="YES" ) %>%
plotPartial(smooth=TRUE, lwd=2, ylab=expression(probability), ylim=c(0.1,1), main=expression(Partial.Dependance.Plot(Random.Forest)), xlab=expression(Age.Head))
# PDP for two variables
m2 %>%
partial(pred.var=c("pres_child", "hhinc"), prob=TRUE, which.class ="YES") %>%
plotPartial(smooth=TRUE, lwd=2, ylab=expression(probability), ylim=c(0.1,1), main=expression(Partial.Dependance.Plot(Random.Forest)), xlab=expression(Presence.Child))
6 Random Forest: Predictive Accuracy in IRI data
set.seed(1001)
indxTrain <- createDataPartition(y = data$purchase,p = 0.70,list = FALSE)
training <- data[indxTrain,]
testing <- data[-indxTrain,]
rfarrest <- randomForest(x=training[,2:10],y=training[,12],data=training,
type="classification",ntree=1000,mtry=2, importance = TRUE)
rfarrest$confusion NO YES class.error
NO 126 179 0.5868852
YES 97 456 0.1754069# Predictive accuracy in training sample
accuracy.train <- rfarrest %>% predict(training)
confusionMatrix(accuracy.train, training$purchase)Confusion Matrix and Statistics
Reference
Prediction NO YES
NO 212 32
YES 93 521
Accuracy : 0.8543
95% CI : (0.8289, 0.8773)
No Information Rate : 0.6445
P-Value [Acc > NIR] : < 2.2e-16
Kappa : 0.6671
Mcnemar's Test P-Value : 8.025e-08
Sensitivity : 0.6951
Specificity : 0.9421
Pos Pred Value : 0.8689
Neg Pred Value : 0.8485
Prevalence : 0.3555
Detection Rate : 0.2471
Detection Prevalence : 0.2844
Balanced Accuracy : 0.8186
'Positive' Class : NO
# Predictive accuracy in testing sample
accuracy.test <- rfarrest %>% predict(testing)
confusionMatrix(accuracy.test, testing$purchase)Confusion Matrix and Statistics
Reference
Prediction NO YES
NO 50 47
YES 80 190
Accuracy : 0.654
95% CI : (0.6028, 0.7026)
No Information Rate : 0.6458
P-Value [Acc > NIR] : 0.394399
Kappa : 0.1976
Mcnemar's Test P-Value : 0.004518
Sensitivity : 0.3846
Specificity : 0.8017
Pos Pred Value : 0.5155
Neg Pred Value : 0.7037
Prevalence : 0.3542
Detection Rate : 0.1362
Detection Prevalence : 0.2643
Balanced Accuracy : 0.5932
'Positive' Class : NO
7 Extreme gradient Boosting: IRI data, Buy or NO BUy
# create tuning grid
grid_default <- expand.grid(nrounds = c(200,300),
max_depth = c(4,5), eta = c(0.01), gamma = c(0,1), min_child_weight = c(10, 25),
colsample_bytree = c(0.7), subsample = c(0.6))
set.seed(123)
# train XGBoost model
xgboost2 <- train(purchase ~ hhinc + hhsize + race + ethnicity +
affluence + pres_child + age_head + educ_fem_head +
census,data=data, tuneGrid = grid_default,
method = "xgbTree", metric ="Accuracy")[19:00:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
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[19:02:10] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:11] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:15] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:18] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:19] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:24] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:27] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:30] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:35] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:37] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:42] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:45] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:50] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:51] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:53] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:02:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:02] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:04] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:10] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:19] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:21] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:27] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:31] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:39] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:43] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:50] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:53] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:03:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:04] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:06] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:10] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:15] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:19] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:27] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:30] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:35] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:37] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:43] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:48] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:51] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:57] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:04:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:06] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.plot(xgboost2)
xgboost2$bestTune nrounds max_depth eta gamma colsample_bytree min_child_weight subsample
9 200 5 0.01 0 0.7 10 0.6xgb.plot.tree(model = xgboost2$finalModel,
trees = 1, plot_width = 800, plot_height = 800)importance_matrix <- xgb.importance(model = xgboost2$finalModel)
print(importance_matrix) Feature Gain Cover Frequency
<char> <num> <num> <num>
1: pres_childYes 0.313255945 0.149982238 0.07957560
2: age_head< 35Y 0.213512031 0.140750397 0.08885942
3: age_head65+Y 0.071533380 0.073617366 0.06100796
4: hhsize4 or more 0.056827456 0.057961415 0.05238727
5: age_head50-54Y 0.034538342 0.046493002 0.04045093
6: educ_fem_headSome or High School 0.031720721 0.056185679 0.06432361
7: raceCaucasian 0.031277181 0.048490198 0.06366048
8: age_head35-44Y 0.028896302 0.041576967 0.05238727
9: age_head45-49Y 0.027824912 0.034404236 0.02188329
10: censusSouth 0.024539377 0.038736697 0.07957560
11: hhsize3 members 0.021220160 0.033321589 0.03580902
12: hhinc$70-99K 0.021092874 0.036584409 0.04310345
13: censusEast 0.019982536 0.031279268 0.03183024
14: educ_fem_headGradauted College 0.016224577 0.036359556 0.06432361
15: educ_fem_headPost College Grade 0.016079962 0.030798136 0.03050398
16: hhinc$50-69K 0.015814372 0.028411720 0.03116711
17: affluenceLiving Comfortably 0.014619607 0.027782896 0.04376658
18: censusCentral 0.014351058 0.029615329 0.04177719
19: hhinc$25-49K 0.013456453 0.026161236 0.03912467
20: affluenceDoing Well 0.008700676 0.019426143 0.02453581
21: ethnicityHispanic 0.002826491 0.006637517 0.00397878
22: hhinc< 25K 0.001705586 0.005424006 0.00596817
Feature Gain Cover Frequencyxgb.plot.importance(importance_matrix = importance_matrix)
8 Extreme gradient Boosting: nhefs data
nhefs <- read_csv(here("data", "nhefs.csv")) %>%
mutate(wt_delta = as.numeric(wt82_71 > median(wt82_71)))
# create tuning grid
grid_default <- expand.grid(nrounds = c(200,300),
max_depth = c(4,5), eta = c(0.01), gamma = c(0,1), min_child_weight = c(10, 25),
colsample_bytree = c(0.7), subsample = c(0.6))
set.seed(123)
# train XGBoost model
xgboost1 <- train(factor(wt_delta) ~ qsmk +
sex + age + income + sbp + dbp + price71 +
tax71 + race, data = nhefs, tuneGrid = grid_default,
method = "xgbTree", metric = "Accuracy")[19:05:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:18] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:24] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:31] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:43] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:50] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:05:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:02] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:11] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:18] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:24] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:42] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:45] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:48] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:50] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:54] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:57] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:06:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:10] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:12] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:35] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:37] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:39] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:43] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:51] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:53] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:07:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:00] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:04] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:08] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:11] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:19] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:21] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:37] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:39] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:40] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:45] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:48] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:51] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:54] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:57] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:08:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:02] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:03] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:06] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:08] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:09] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:11] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:15] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:16] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:18] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:21] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:26] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:27] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:31] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:33] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:39] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:43] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:44] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:46] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:47] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:49] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:50] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:52] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:53] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:55] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:56] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:58] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:09:59] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:01] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:02] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:04] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:05] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:07] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:08] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:10] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:11] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:13] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:14] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:15] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:17] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:18] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:20] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:21] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:22] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:23] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:25] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:27] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:28] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:29] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:31] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:32] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:34] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:35] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:36] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:38] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:39] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:41] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.
[19:10:42] WARNING: src/c_api/c_api.cc:935: `ntree_limit` is deprecated, use `iteration_range` instead.# plot(xgboost1)
xgboost1$bestTune nrounds max_depth eta gamma colsample_bytree min_child_weight subsample
15 200 5 0.01 1 0.7 25 0.6xgb.plot.tree(model = xgboost1$finalModel,
trees = 1:2, plot_width = 800, plot_height = 800)importance_matrix <- xgb.importance(model = xgboost1$finalModel)
print(importance_matrix) Feature Gain Cover Frequency
<char> <num> <num> <num>
1: age 0.458471328 0.32119934 0.281146637
2: dbp 0.153948154 0.16985337 0.171995590
3: qsmk 0.140593604 0.14179957 0.108048512
4: sbp 0.096442882 0.13536373 0.153252481
5: price71 0.061374316 0.09701480 0.127894157
6: income 0.046092537 0.06665409 0.072767365
7: sex 0.022381198 0.03164424 0.044101433
8: tax71 0.015433740 0.02554422 0.033076075
9: race 0.005262242 0.01092664 0.007717751xgb.plot.importance(importance_matrix = importance_matrix)